Research workbench
Cryo-EM structure of human MLL1-ncp complex, binding MODE2
Analyse Cryo-EM structure of human MLL1-ncp complex, binding MODE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KIZ
- Type
- protein + DNA
- Length
- 2,051 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B 1.1; DNA (145-mer)…
- EC
- 2.1.1.43
- UniProt
- A0A310TTQ1, P62799, Q6AZJ8, P02281, Q15291, Q03164, P61964, Q9UBL3
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 13 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3 | protein | 97 | 65% helix, 4% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 82 | 59% helix, 9% strand | P62799 |
| C | Histone H2A | protein | 107 | 51% helix, 3% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 94 | 72% helix, 2% strand | P02281 |
| F | Histone H4 | protein | 78 | 65% helix, 6% strand | P62799 |
| G | Histone H2A | protein | 105 | 52% helix, 5% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 95 | 74% helix, 2% strand | P02281 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| N | Retinoblastoma-binding protein 5 | protein | 351 | 2% helix, 33% strand | Q15291 |
| K | Histone-lysine N-methyltransferase 2A (EC 2.1.1.43) | protein | 179 | 17% helix, 24% strand | Q03164 |
| R | Wd repeat-containing protein 5 | protein | 300 | 0% helix, 43% strand | P61964 |
| T | SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 176 | 2% helix, 26% strand | Q9UBL3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.78 | 0.80 | 67 | empty |
| 2 | 643 | 0.76 | 0.82 | 52 | empty |
| 3 | 1161 | 0.75 | 0.78 | 71 | empty |
| 4 | 695 | 0.74 | 0.80 | 63 | empty |
| 5 | 648 | 0.74 | 0.81 | 54 | empty |
Interfaces
43 interfaces between chains.
- I–J · 6676 Ų buried · 619 hydrogen bonds · nucleic-nucleic
- G–H · 2626 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2548 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2501 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 2402 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6KIZ · Cryo-EM structure of human MLL1-NCP complex, binding mode2 · the same entry in another collection · chain T against T, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt Q15291
- Every structure of UniProt Q03164
- Every structure of UniProt P61964
- Every structure of UniProt Q9UBL3
- Elsewhere: RCSB PDB 6KIZ · PDBe 6KIZ · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt Q15291 · UniProt Q03164 · UniProt P61964 · UniProt Q9UBL3
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